Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori
Background: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of e...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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BioMed Central
2005
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| _version_ | 1797053935867920384 |
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| author | Saunders, N Boonmee, P Peden, J Jarvis, S |
| author_facet | Saunders, N Boonmee, P Peden, J Jarvis, S |
| author_sort | Saunders, N |
| collection | OXFORD |
| description | Background: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. Results: This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. Conclusion: New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation. |
| first_indexed | 2024-03-06T18:50:33Z |
| format | Journal article |
| id | oxford-uuid:1011acd1-d976-439e-8a20-d72372deff4b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T18:50:33Z |
| publishDate | 2005 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:1011acd1-d976-439e-8a20-d72372deff4b2022-03-26T09:54:30ZInter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pyloriJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:1011acd1-d976-439e-8a20-d72372deff4bPathologyEnglishOxford University Research Archive - ValetBioMed Central2005Saunders, NBoonmee, PPeden, JJarvis, SBackground: Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. Results: This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. Conclusion: New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation. |
| spellingShingle | Pathology Saunders, N Boonmee, P Peden, J Jarvis, S Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
| title | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
| title_full | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
| title_fullStr | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
| title_full_unstemmed | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
| title_short | Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori |
| title_sort | inter species horizontal transfer resulting in core genome and niche adaptive variation within helicobacter pylori |
| topic | Pathology |
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